- Trendspotting in the Protein Data Bank
(2013) FEBS Lett. 587: 1036-45
doi:10.1016/j.febslet.2012.12.029
- The Future of the Protein Data Bank
(2013) Biopolymers 99: 218-222
doi:10.1002/bip.22132
- The RCSB Protein Data Bank: new resources for research and education
(2013) Nucleic Acids Research 41: D475-D482
doi:10.1093/nar/gks1200
- Illustrating the Machinery of Life: Viruses
(2012) Biochemistry and Molecular Biology Education 40: 291-296
doi:10.1002/bmb.20636
- Putting proteins in context: scientific illustrations bring together
information from diverse sources to provide an integrative view of the
molecular biology of cells
(2012) Bioessays 34(9):718-20
doi:10.1002/bies.201200072
- Creating a community resource for protein science
(2012) Protein Science 21: 1587-1596
doi:10.1002/pro.2154
- BioJava: an open-source framework for bioinformatics in 2012
(2012) Bioinformatics 28: 2693-2695
doi:10.1093/bioinformatics/bts494
- Outcome of the first electron microscopy validation task force meeting
(2012) Structure 20: 205-214
doi:10.1016/j.str.2011.12.014
- The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future
(2012) Structure 20: 391-396
doi:10.1016/j.str.2012.01.010
- The Worldwide Protein Data Bank
In International Tables for X-Ray Crystallography, Volume F:
Crystallography of biological macromolecules
E. Arnold, D. M. Himmel & M. G. Rossmann, editors
(2012) Springer, Dordrecht, The Netherlands, pp. 827-832
doi:10.1107/97809553602060000111
- Circular Permutation in Proteins
(2012) PLoS Comput Bio 8: e1002445
doi:10.1371/journal.pcbi.1002445
- Atomic evidence: the foundations of structural molecular biology
(2011) Science Progress 94: 414-430
doi:10.3184/003685011X13201799666745
- The evolution of the Protein Data Bank (part of special essay collection on the 40th anniversary of the PDB)
(2011) Nature Structural & Molecular Biology 18: 1310
doi:10.1038/nsmb1211-1304
- Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction
(2011) Proteins: Structure, Function, and Bioinformatics 79: 6-20
doi:10.1002/prot.23196
- A new generation of crystallographic validation tools for the Protein Data Bank
(2011) Structure 19: 1395-1412
doi:10.1016/j.str.2011.08.006
- The Protein Data Bank
in Leadership in Science and Technology: A Reference Handbook,
William Sims Bainbridge, editor (2012) SAGE Publications, Inc., Thousand Oaks, CA.,
volume 2, pages 661-675.
- Miniseries: Illustrating the machinery of life: Eukaryotic cell panorama
(2011) Biochem Mol Biol Educ. 39:91-101
doi:10.1002/bmb.20494
- The evolution of the RCSB Protein Data Bank website
(2011) WIREs Computational Molecular Science 1: 782-789
doi:10.1002/wcms.57
- The RCSB Protein Data Bank: site functionality and bioinformatics use cases
(2011) NCI-Nature Pathway Interaction Database
doi:10.1038/pid.2011.1
- Quality assurance for the query and distribution systems of the RCSB Protein Data Bank
(2011) Database
doi:10.1093/database/bar003
- The RCSB Protein Data Bank: redesigned web site and web services
(2011) Nucleic Acids Res. 39: D392-D401
doi:10.1093/nar/gkq1021
- The Protein Data Bank: Exploring Biomolecular Structure
(2010) Nature Education 3:39.
- Precalculated Protein Structure Alignments at the RCSB PDB website
(2010) Bioinformatics 26: 2983-2985
doi: 10.1093/bioinformatics/btq572
- Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences
J. Appl. Cryst. (2010) 43:1224-1229
doi:10.1107/S002188981002371X
- Getting the Most Out of the Protein Data Bank
(2010) The Journal of Biocommunication 35: E52-E57.
- dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction
of a consensus assignment
BMC Bioinformatics (2010) 11:310.
doi:10.1186/1471-2105-11-310
- Integration of open access literature into the RCSB Protein Data Bank Using BioLit
BMC Bioinformatics (2010) 11:220.
doi:10.1186/1471-2105-11-220
- Will Widgets and Semantic Tagging Change Computational Biology?
PLoS Comput Biol (2010) 6(2): e1000673. doi:10.1371/journal.pcbi.1000673
- Data Deposition and Annotation at the Worldwide Protein Data Bank
Mol Biotechnol (2009) 42:1-13.
doi: 10.1007/s12033-008-9127-7
-
The PDB format, mmCIF formats, and other data formats
in
Structural Bioinformatics,
second edition
Gu and Bourne, eds.
(2009) John Wiley & Sons, Inc., Hoboken, NJ, pp 271-291
-
The Worldwide Protein Data Bank
in Structural
Bioinformatics,
second edition
Gu and Bourne, eds.
(2009) John
Wiley & Sons, Inc., Hoboken, NJ, pp 293-303.
-
Outcome of a Workshop on Applications of Protein Models in Biomedical Research
(2009) Structure 17: 151-159.
-
Representation of viruses in the remediated PDB archive
(2008) Acta Cryst. D64: 874-882
doi: 10.1107/S0907444908017393
-
Interesting Structures: Education and Outreach at the RCSB Protein Data Bank
(2008) PLoS Biology 6:e117.
doi: 10.1371/journal.pbio.0060117
- Data deposition and annotation at the Worldwide Protein Data Bank
(2008) Methods in Molecular Biology, vol. 426:
Structural
Proteomics: High-Throughput Methods
-
BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank
(wwPDB): new policies affecting biomolecular NMR depositions
(2008) J Biomol NMR 40(3): 153-155
-
Remediation of the Protein Data Bank archive
(2008) Nucleic Acids Research 36: D426-433. doi: 10.1093/nar/gkm937
-
The Protein Data Bank: a historical perspective
(2008) Acta Cryst. A64: 88-95. doi: 10.1107/S0108767307035623
-
Using the Tools and Resources of the RCSB Protein Data Bank
(2007) Current Protocols in Bioinformatics 1.9.1-1.9.24. doi: 10.1002/0471250953.bi0109s20
-
A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing.
(2007) Proteins 69(3): 449-65. doi: 10.1002/prot.21507
-
Realism about PDB
(2007) Nature Biotechnology 25: 845-846.
- The Research Collaboratory for Structural Bioinformatics Protein Data Bank
(2007) Comprehensive Medicinal Chemistry II, Vol. 3, Drug Discovery Technologies, H. Kubinyi, Ed, Elsevier, Oxford, UK pp. 373-388.
-
The Worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data.
(2007) Nucleic Acids Res. 35(Database issue): D301-3.
-
A Biocurator Perspective: Annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank
(2006) PLoS Comput Biol 2(10): e99
- Archiving structural models of biological macromolecules: outcome of a workshop on biological macromolecular structure models
(2006) Structure, 14: 1211-1217.
- Partitioning protein structures into domains: Why is it so difficult?
(2006) J Mol Biol, 361(3): 562-90. doi: 10.1016/j.jmb.2006.05.060
|
- Reflections on the science and law of structural
biology, genomics, and drug development
(2006) UCLA Law Review, 53: 871 - 908.
- Using the Tools and Resources of the RCSB Protein Data Bank
(2005) Current Protocols in Bioinformatics 1.9.1-1.9.40. doi: 10.1002/0471250953.bi0109s20
- The RCSB PDB information portal for structural
genomics
Describes the online tools, summary reports, and target information
related to structural genomics from a new information portal at sg.pdb.org.
(2006) Nucleic Acids Research, Vol. 34, Database issue D302-D305.
- The Molecular Biology Toolkit (MBT):
A Modular Platform for Developing Molecular Visualization Applications
(2005) BMC Bioinformatics, 6: 21.
- Functional coverage of the human genome by existing
structures, structural genomics targets, and homology models.
(2005) PLoS Comp Biol 1(3): e31.
- PDBML: the representation of archival macromolecular
structure data in XML.
(2005) Bioinformatics 21, pp. 988-992.
- Large Macromolecular Complexes in the Protein Data
Bank: A Status Report
(2005) Structure 13, pp. 381-388. doi: 10.1016/j.str.2005.01.008
- The RCSB Protein Data Bank: a redesigned query
system and relational database based on the mmCIF schema
(2005) Nucl. Acids Res 33: D233-D237.
- DDL2 dictionary, in International Tables for Crystallography
J.D. Westbrook and S.R. Hall, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. (2005) Springer: Dordrecht, The Netherlands. pp. 473-481.
- The Macromolecular dictionary (mmCIF), in International Tables for Crystallography, Volume G
P.M.D. Fitzgerald, J.D. Westbrook, P.E. Bourne, B. McMahon, K.D. Watenpaugh, and H.M. Berman, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. (2005) Springer: Dordrecht, The Netherlands. pp. 295-443.
-
Classification and use of macromolecular data,
in International Tables for Crystallography, Volume G
P.M.D. Fitzgerald, J.D. Westbrook, P.E. Bourne, B. McMahon, K.D. Watenpaugh, and H.M. Berman, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. 2005, Springer: Dordrecht, The Netherlands. p. 144-198.
- Specification of a relational Dictionary Definition Language (DDL2), in International Tables for Crystallography, Volume G
J.D. Westbrook, H.M. Berman, and S.R. Hall, , G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. (2005) Springer: Dordrecht, The Netherlands. pp. 61-72.
- The use of mmCIF architecture for PDB data management, in International Tables for Crystallography, Volume G
J. Westbrook, H. Yang, Z. Feng, and H.M. Berman, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. 2005, Springer: Dordrecht, The Netherlands. p. 539-543.
- The Protein Data Bank exchange data dictionary,
in International Tables for Crystallography, Volume G
J. Westbrook, K. Henrick, E.L. Ulrich, and H.M. Berman, G. Definition
and exchange of crystallographic data, S.R. Hall and B. McMahon,
Editors. (2005) Springer: Dordrecht, The Netherlands. pp. 195-198. PDF Version
- Image dictionary (imgCIF), in International Tables for Crystallography, Volume G
A.P. Hammersley, H.J. Bernstein, and J.D. Westbrook, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. (2005) Springer: Dordrecht, The Netherlands. pp. 444-459.
- Specification of the Crystallographic Information File, in International Tables for Crystallography, Volume G
S.R. Hall and J.D. Westbrook, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. (2005) Springer: Dordrecht, The Netherlands. pp. 20-36.
- Formal specification of the Crystallographic Information File, in International Tables for Crystallography, Volume G
S.R. Hall, N. Spadaccini, I.D. Brown, H.J. Bernstein, J.D. Westbrook, and B. McMahon, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. (2005) Springer: Dordrecht, The Netherlands. pp. 25-36.
- TargetDB:
a target registration database for structural genomics projects
(2004) Bioinformatics 20, pp. 2860-2862.
- Automated
and accurate deposition of structures solved by X-ray diffraction to
the Protein Data Bank
(2004) Acta Cryst. D60, pp. 1833-1839.
- Ligand
Depot: a data warehouse for ligands bound to macromolecules
Ligand Depot is an integrated data resource for finding information
about small molecules bound to proteins and nucleic acids. (2004) Bioinformatics
20, pp. 2153-2155.
- The Impact of
Structural Genomics on the Protein Data Bank (2004)
Am. J. PharmacoGenomics 4, pp. 247-252.
- The Protein Data
Bank and lessons in data management
(2004) Briefings in Bioinformatics 5, pp 23-30. doi: 10.1093/bib/5.1.23
- The PDB: A case study in management of community data
Published in the inaugural issue of Current Proteomics. (2004) Current Proteomics 1, pp. 49-57.
- Validation of protein structures for the PDB
(2003) Methods Enzymol. 374, pp. 370-85. doi: 10.1016/S0076-6879(03)74017-8
- The distribution and query systems of the RCSB Protein Data Bank
(2003) Nucleic Acids Research, 32, pp. D223-5. doi: 10.1093/nar/gkh096
- Announcing the worldwide Protein Data Bank
(2003) Nature Structural Biology, 10 (12), p. 980. doi: 10.1038/nsb1203-980
- The Protein Data Bank
P. E. Bourne and H. Weissig. Hoboken, NJ, John Wiley & Sons, Inc. pp. 181-198.
- The PDB format, mmCIF formats and other data formats.
P. E. Bourne and H. Weissig. Hoboken, NJ, John
Wiley & Sons, Inc. pp. 161-179.
- The Protein Data Bank and structural genomics
(2003) Nucleic Acids Research 31, pp. 489-491. doi: 10.1093/nar/gkg068
- An ontology driven architecture for derived representations of macromolecular structure
(2002) Bioinformatics 18 (9), pp. 1280-1281. Oxford University Press. doi: 10.1093/bioinformatics/18.9.1280
- The CCPN project: an interim report on a data model for the NMR community
(2002) Nature Structural Biology 9 (6), pp. 416-418. doi: 10.1038/nsb0602-416
- Protein Structures: From Famine to Feast
(2002) American Scientist 90 (4), pp. 350 - 359. doi: 10.1511/2002.4.350
- The Protein Data Bank
(2002) Acta Cryst. D 58 (6:1), pp. 899-907. doi: 10.1107/S0907444902003451
- Protein structure resources
(2002) Acta Cryst. D 58 (6:1), pp. 908-915. doi: 10.1107/S0907444902003906
- The Protein Data Bank: unifying the archive
(2002) Nucleic Acids Research, 30 (1), pp. 245-248. doi: 10.1093/nar/30.1.245
- The Protein Data Bank, 2001 -
(2001) In International Tables for Crystallography (M. G. Rossman & E. Arnold, eds.), Vol. F. Crystallography of Biological Macromolecules, pp. 675-662. Kluwer Academic Publishers, Dordrecht.
- The PDB data uniformity project
(2001) Nucleic Acids Research, 29: 214-218. doi: 10.1093/nar/29.1.214
- The Protein Data Bank and the challenge of structural genomics
(2000) Nature Structural Biology, 7 (11), pp. 957-959. doi: 10.1038/80734
- The Protein Data Bank
(2000) Nucleic Acids Research 28: 235-242. doi: 10.1093/nar/28.1.235
Reference for the RCSB PDB.
|